福清山羊与努比亚黑山羊背最长肌比较转录组分析

doi:10.3864/j.issn.0578-1752.2019.14.011

Abstract

Abstract:

【Objective】The aim of this study was to analyze the transcriptome differentially genes expression of longissimus doris tissue in Fuqing goat and Nubian Black goat.【Method】 Two goat breeds, including Fuqing goat and Nubian Black goat, were used as experimental animal, and fatten of castrated ram were used as experimental samples. We determined the samples’ADG in 12 months, and IMF content in longissimus doris tissue at the age of 12 months. Transcriptome sequencing of longissimus doris tissue in Fuqing goat and Nubian Black goat were performed by using the Illumina HiSeq ^TM 2500 platform with 3 biological replicates per goat breed, and verified by quantitative real-time PCR (qRT-PCR). Differentially expressed genes (DEGs) were selected and enriched based on GO and COG and KEGG database. 【Result】 By fatten of castrated ram, the ADG of Nubiya Black goats in 12 months was higher that of Fuqing goats (Sig.=0.000). But, the IMF content in longissimus doris tissue of Fuqing goats at age of 12 months was higher than that of Nubiya Black goat (Sig.=0.003). A total of 44.76 Gb clean data were obtained in six samples. We found 608 DEGs between Fuqing goat and Nubian Black goat, including 61 DEGs up-regulated genes and 547 DEGs down-regulated genes. Moreover, 518 DEGs and 148 DEGs and 418 DEGs were enriched by GO and COG and KEGG database, respectively. KEGG pathway analysis showed that DEGs annotated to 222 metabolic pathways, and 44 pathways were enriched significantly, such as regulation of actin cytoskeleton, and Jak-STAT signaling pathway, and MAPK signaling pathway and Type Ⅰdiabetes mellitus associated with meat quality and growth traits in goat. The results showed that 8 DEGs (IGF1, ACSL5, PCK2, PPARGC1A, JAK2, STAT4, IRF8 and MAP4K1) might relate to meat quality and growth traits of goat were screened by GO functional enrichment and KEGG Pathway analysis. In addition, 707 new genes or transcripts were found by BLAST, including 15 DEGs between two breeds. By qRT-PCR verification, the pattern of selected genes was consistent with the results of transcriptome sequencing, which showed the sequencing results were reliable. 【Conclusion】Totally, 608 DEGs and 707 new genes of longissimus doris tissue in Fuqing goat and Nubian Black goat were screened by transcriptional analysis, and revealed that four pathways might play an important role in goat meat quality and growth traits.

Key words: Fuqing goat, Nubian Black goat, longissimus doris, differentially expressed genes, transcriptome

LIU Yuan,LI WenYang,WU XianFeng,HUANG QinLou,GAO ChengFang,CHEN XinZhu,ZHANG XiaoPei. Transcriptome Analysis of Differentially Gene Expression Associated with longissimus doris Tissue in Fuqing Goat and Nubian Black Goat[J].Scientia Agricultura Sinica, 2019, 52(14): 2525-2537.

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References 40

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基因名称 Gene	上游引物 Forward primer（5′-3′）	下游引物 Reverse primer（5′-3′）	产物长度 Product size（bp）
18S rRNA	GTAACCCGTTGAACCCCATT	CCATCCAATCGGTAGTAGCG	151
TMSSF2	TAGGATCTCTGTGGCGCACC	TTCCGAATGGACTGGTTGGA	108
CD52	AGAAGCACCCCCAATCCTTG	GAACCTCCCTGTGTCAGCCA	105
TASR 1	ACAGGAGAGGCCAGGTTGTA	ACTGTGTCTCCCACAGTGCA	101
GN-1377	CCCGATTCGGTGACATGTTC	TTCCGTCGGTTTTGGAGTTG	105
GN-1378	GTCAGTGATCGTGTTCCGCA	TCTCAGGCTGTCGGTGACCT	101
GN-1272	GGAGACCCAGAGAGCAAAGA	TGTTGACAGCGTCTGCTTTC	117
MyHCⅠ	AAGAACCTGCTGCGGCTG	CCAAGATGTGGCACGGCT	250
MyHCⅡb	GACAACTCCTCTCGCTTTGG	GGACTGTGATCTCCCCTTGA	247

样品 Sample	F1	F2	F3	平均值 Mean	N4	N5	N6	平均值 Mean	t	P值 P-value
初生重 Birth weight (kg)	1.31	1.24	1.37	1.31±0.07	3.25	3.47	3.52	3.41±0.14	-23.14	0.000
宰前活重 Body Weight (kg)	24.8	25.3	25.5	25.2±0.36	48.2	51.4	49.7	49.8±1.6	-25.93	0.000
平均日增重 ADG(g.d^-1)	64.5	66.1	66.3	65.6±0.99	123.5	131.7	126.9	127.4±4.12	-25.24	0.000
IMF(%)	3.11	3.94	4.03	3.69±0.51	1.79	1.73	1.97	1.83±0.12	6.18	0.003

样品 Sample	总Reads Total reads	可定位的Reads Mapped reads	唯一定位Reads Uniq mapped reads	多点定位Reads Multiple mapped reads
F1	48425148	41178058/85.03%	38498938/79.50%	2679120/5.53%
F2	52036998	44841490/86.17%	42130532/80.96%	2710958/5.21%
F3	45474102	38872827/85.48%	37033407/81.44%	1839420/4.04%
N4	47876820	40525347/84.65%	38452657/80.32%	2072690/4.33%
N5	52575764	44743681/85.10%	42129626/80.13%	2614055/4.97%
N6	53888214	45906932/85.19%	43520461/80.76%	2386471/4.43%

基因 Gene	转录组测序RNA-Seq	荧光定量PCR Real-time PCR
基因 Gene	表达倍数(福清山羊/努比亚黑山羊) log₂FC (Fuqing goats/Nubian Black goats)	表达倍数(福清山羊/努比亚黑山羊) log₂FC (Fuqing goats/Nubian Black goats)
TMSSF2	-2.41±0.93	-2.90±2.51
CD52	2.48±0.56	2.60±1.37
TASR1	3.43±2.61	1.80±0.86
GN-1377	2.51±1.20	0.98±0.76
GN-1378	2.73±0.33	1.08±0.41
GN-1272	1.22±1.00	1.07±0.68
MyHcⅠ	-0.24±1.04	-0.11±1.36
MyHcⅡb	-0.62±0.39	-0.51±1.22

Transcriptome Analysis of Differentially Gene Expression Associated with longissimus doris Tissue in Fuqing Goat and Nubian Black Goat

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